Mattenklee landraces are persistent and locally adapted Swiss red clover populations. About 100 populations are preserved and may represent a significant yet poorly characterised genetic resource for temperate regions. Genetic characterisation is important in order to improve cultivars, manage genetic resources and to maintain or restore biodiversity. The objectives of this study were to analyse genetic diversity, investigate potential ancestry and to elucidate the congruence of phenotypic and genetic structure of Mattenklee landraces